As far as I know there is no way to 'place' these effects. They are hardlinked to the engine positions and those are taken from the aircraft.cfg. But as said, I have seen issues here before. For example contrails that start 100 meter in front of the aircraft.
In a case like this I would suggest looking at the calibration screen in the sim. That will show if the software is doing what the hardware tells is or that there is another problem. Do keep us informed!